Comparative population genomic analyses of the reconstructed local breed “Nero di Parma” with other commercial and autochthonous Italian pig breeds

Abstract

Most of the Italian pig genetic resources that existed at the beginning of the last century have been substituted by more productive populations. At present, only six original autochthonous pig breeds are officially recognized in Italy and have their own herd books managed by the National Pig Breeders Association. Another section of the breed herd book includes breeds that were completely lost but that were subsequently reconstructed through specific crossbreeding programmes. This is the case of the Nero di Parma breed that was officially recognized as reconstructed breed in 2016. This is a small breed, reared in the province of Parma (North of Italy), that accounts for 103 and 12 registered sow and boars, respectively. In this study, using single nucleotide polymorphisms genotyped with the Illumina PorcineSNP60 BeadChip array, we compared, at the genome level, the reconstructed Nero di Parma pig breed with three Italian commercial (Italian Large White, Italian Duroc and Italian Landrace) and four autochthonous (Apulo-Calabrese, Casertana, Cinta Senese and Nero Siciliano) pig breeds. Nero di Parma showed the highest level of linkage disequilibrium among all analysed breeds. Effective population size estimated over past generations was the lowest in this reconstructed breed. However, genomic inbreeding parameters did not suggest a high level of inbreeding in Nero di Parma. The comparative analysis against several other Italian pig breeds made it possible to evaluate the obtained information that could be helpful to define potential future conservation and breeding strategies for this small reconstructed breed.